Selected locus and multiple panel models for radiation hybrid mapping.

We develop two new types of models for whole-genome radiation hybrid mapping using the general multipoint framework. The first, selected locus models, are appropriate for mapping markers in the region of a selectable locus that was used in creation of the hybrids. The models allow for strong retention of the selectable locus, with retention rates decreasing with increasing distance from the selectable locus in both directions. We illustrate the application of these models with 10 chromosome 17 sequence-tagged site (STS) markers and the thymidine kinase (TK) locus typed on a whole-genome hybrid panel in which TK was used in the selection process. The second set of models are appropriate when loci typed on two or more independent panels are to be used to build maps. Maps can be built assuming interlocus distances are independent or proportional between the panels, and the hypothesis of proportional distances can be tested. We illustrate the application of these models by using 27 chromosome 21 STS markers typed on two hybrid panels created with radiation doses of approximately 10,000 and approximately 50,000 Rads.     

Unusual chromatin in human telomeres.

We report that human telomeres have an unusual chromatin structure characterized by diffuse micrococcal nuclease patterns. The altered chromatin manifested itself only in human telomeres that are relatively short (2 to 7 kb). In contrast, human and mouse telomeres with telomeric repeat arrays of 14 to 150 kb displayed a more canonical chromatin structure with extensive arrays of tightly packed nucleosomes. All telomeric nucleosomes showed a shorter repeat size than bulk nucleosomes, and telomeric mononucleosomal particles were found to be hypersensitive to micrococcal nuclease. However, telomeric nucleosomes were similar to bulk nucleosomes in the rate at which they sedimented through sucrose gradients. We speculate that mammalian telomeres have a bipartite structure with unusual chromatin near the telomere terminus and a more canonical nucleosomal organization in the proximal part of the telomere.     

Carotenoid composition and metabolism in green and blue-green algal lichens in the field

The carotenoid composition of 33 species of green algal lichens and 5 species of blue-green algal lichens was examined and compared with that of the leaves of higher plants. As in higher plants, green algal lichen species which were found in both shade and full sunlight exhibited higher levels of the carotenoids involved in photoprotective thermal energy dissipation (zeaxanthin as well as the total xanthophyll cycle pool) in the sun than in the shade. This was particularly true when thalli were moist during exposure to high light, or presumably became desiccated in full sunlight. However, the reverse trend in the carotenoid composition of green algal lichens was also observed in those species which were found predominantly either in the shade or in full sunlight. In this case sun-exposed lichens often possessed lower levels of zeaxanthin and of the components of the xanthophyll cycle than lichens which were found in the shade. In contrast to higher plants, the lichens from all habitats exhibited a relatively high ratio of carotenoids to chlorophylls (more characteristic of sun leaves), very low levels of α-carotene (similar to that found in sun leaves), and a level of β-carotene similar to that found in shade leaves. Zeaxanthin, but not the expoxides of the xanthophyll cycle, was also frequently found in blue-green algal lichens. A trend for increasing levels of zeaxanthin with increasing growth light regime was observed inPeltigera rufescens, the species which was found to occur over the widest range of light environments. The level of zeaxanthin per chlorophylla in these blue-green algal lichens was in a range similar to that per chlorophylla+b in green algal lichens. However, zeaxanthin was also absent in one species,Collema cristatum, in full sunlight. Thus, the zeaxanthin content of the blue-green algal lichens can be similar to that of higher plants, or it can be rather dissimilar, as was also the case in the green algal lichen species. The presence of large amounts of ketocarotenoids in blue-green algal lichens is also noteworthy.     

Temperate rainforest lichens in New Zealand: high thallus water content can severely limit photosynthetic CO2 exchange

CO₂ exchange rate in relation to thallus water content (WC, % of dry weight) was determined for 22 species of lichens, mainly members of the genera Pseudocyphellaria and Sticta, from a temperate rainforest, Urewere National Park, New Zealand. All data were obtained in the field, either using a standard technique in which the lichens were initially wetted (soaked or sprayed, then shaken) and allowed to slowly dry, or from periodic measurements on samples that were continuously exposed in their natural habitat. A wide range of WC was found, with species varying from 357 to 3360% for maximal WC in the field, and from 86 to 1300% for optimal WC for photosynthesis. Maximal WC for lichens, wetted by the standard technique, were almost always much less than the field maxima, due to the presence of water on the thalli. The relationships between CO₂ exchange rate and WC could be divided into four response types based on the presence, and degree, of depression of photosynthesis at high WC. Type A lichens showed no depression, and Type B only a little at maximal WC. Type C had a very large depression and, at the highest WC, CO₂ release could occur even in the light. Photosynthetic depression commenced soon after optimal WC was reached. Type D lichens showed a similar depression but the response curve had an inflection so that net photosynthesis was low but almost constant, and never negative, at higher WC. There was little apparent relationship between lichen genus or photobiont type and the response type. It was shown that high WC does limit photosynthetic CO₂ uptake under natural conditions. Lichens, taken directly from the field and allowed to dry under controlled conditions, had net photosynthesis rates that were initially strongly inhibited but rose to an optimum, before declining at low WC. The limiting effects of high WC were clearly shown when, under similar light conditions, severe photosynthetic depression followed a brief, midday, rain storm. Over the whole measuring period the lichens were rarely at their optimal WC for photosynthesis, being mostly too wet or, occasionally, too dry. Photosynthetic performance by the lichens exposed in the field was similar to that expected from the relationship between the photosynthetic rate and WC established by the standard procedure.     

Match probabilities in racially admixed populations.

The calculation of match probabilities is the most contentious issue dividing prosecution and defense experts in the forensic applications of DNA fingerprinting. In particular, defense experts question the applicability of the population genetic laws of Hardy-Weinberg and linkage equilibrium to racially admixed American populations. Linkage equilibrium justifies the product rule for computing match probabilities across loci. The present paper suggests a method of bounding match probabilities that depends on modeling gene descent from ancestral populations to contemporary populations under the assumptions of Hardy-Weinberg and linkage equilibrium only in the ancestral populations. Although these bounds are conservative from the defendant's perspective, they should be small enough in practice to satisfy prosecutors.     

Biosynthesis of 12α-and 13-hydroxylated gibberellins in a cell-free system from Cucurbita maxima endosperm and the identification of new endogenous gibberellins

Gibberellin (GA) biosynthesis in cell-free systems from Cucurbita maxima L. endosperm was reinvestigated using incubation conditions different from those employed in previous work. The metabolism of GA₁₂ yielded GA₁₃, GA₄₃ and 12α-hydroxyGA₄₃ as major products, GA₄, GA₃₇, GA₃₉, GA₄₆ and four unidentified compounds as minor products. The intermediates GA₁₅, GA₂₄ and GA₂₅ accumulated at low protein concentrations. The structure of the previously uncharacterised 12α-hydroxyGA₄₃ was inferred from its mass spectrum and by its formation from both GA₃₉ and GA₄₃. Gibberellin A₃₉ and 12α-hydroxyGA₄₃ were formed by a soluble 12α-hydroxylase that had not been detected before. Gibberellin A₁₂-aldehyde was metabolised to essentially the same products as GA₁₂ but with less efficiency. A new 13-hydroxylation pathway was found. Gibberellin A₅₃, formed from GA₁₂ by a microsomal oxidase, was converted by soluble 2-oxoglutarate-dependent oxidases to GA₁ GA₂₃, GA₂₈, GA₄₄, and putative 2β-hydroxyGA₂₈. Minor products were GA₁₉, GA₂₀, GA₃₈ and three unidentified GAs. Microsomal 13-hydroxylation (the formation of GA₅₃) was suppressed by the cofactors for 2-oxoglutarate-dependent enzymes. Reinvestigation of the endogenous GAs confirmed the significance of the new metabolic products. In addition to the endogenous GAs reported by Blechschmidt et al. (1984, Phytochemistry 23, 553–558), GA₁, GA₈, GA₂₅, GA₂₈, GA₃₆, GA₄₈ and 12α-hydroxyGA₄₃ were identified by full-scan capillary gas chromatography-mass spectrometry and Kovats retention indices. Thus both the 12α-hydroxylation and the 13-hydroxylation pathways found in the cell-free system operate also in vivo, giving rise to 12α-hydroxyGA₄₃ and GA₁ (or GA₈), respectively, as their end products. Evidence for endogenous GA₂₀ and GA₂₄ was also obtained but it was less conclusive due to interference.     

Ecological and methodological drivers of non-stationarity in tree growth response to climate

Radial tree growth is sensitive to environmental conditions, making observed growth increments an important indicator of climate change effects on forest growth. However, unprecedented climate variability could lead to non-stationarity, that is, a decoupling of tree growth responses from climate over time, potentially inducing biases in climate reconstructions and forest growth projections. Little is known about whether and to what extent environmental conditions, species, and model type and resolution affect the occurrence and magnitude of non-stationarity. To systematically assess potential drivers of non-stationarity, we compiled tree-ring width chronologies of two conifer species, Picea abies and Pinus sylvestris, distributed across cold, dry, and mixed climates. We analyzed 147 sites across the Europe including the distribution margins of these species as well as moderate sites. We calibrated four numerical models (linear vs. non-linear, daily vs. monthly resolution) to simulate growth chronologies based on temperature and soil moisture data. Climate–growth models were tested in independent verification periods to quantify their non-stationarity, which was assessed based on bootstrapped transfer function stability tests. The degree of non-stationarity varied between species, site climatic conditions, and models. Chronologies of P. sylvestris showed stronger non-stationarity compared with Picea abies stands with a high degree of stationarity. Sites with mixed climatic signals were most affected by non-stationarity compared with sites sampled at cold and dry species distribution margins. Moreover, linear models with daily resolution exhibited greater non-stationarity compared with monthly-resolved non-linear models. We conclude that non-stationarity in climate–growth responses is a multifactorial phenomenon driven by the interaction of site climatic conditions, tree species, and methodological features of the modeling approach. Given the existence of multiple drivers and the frequent occurrence of non-stationarity, we recommend that temporal non-stationarity rather than stationarity should be considered as the baseline model of climate–growth response for temperate forests.     

Zoosporogenesis in Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew

During sporulation of Pseudoperonospora cubensis on cucumber leaves ( Cucumis saliva ) zoosporangia are formed on the dichotomously branched sporangiophore. The mature zoosporangium has a preformed discharge papilla and the cytoplasm is uncleaved. The zoosporangium wall is decorated and the outer layer of the wall is electron opaque in ultrathin sections. As the zoosporangium is able to survive freezing (- 18°C) for prolonged periods of time (3–4 months) the zoosporangium may serve as the "resting" structure which survives overwintering in Northern latitudes in the absence of oospore formation.
Zoospore cleavage can be synchronized by placing freshly harvested zoosporangia in distilled water. Cleavage of the zoosporangial cytoplasm is by means of the fusion of small vesicles apparently derived from dictyosomes which become highly active after zoosporogenesis is induced.
Vesicles with an osmiophilic electron opaque content are the dominant type of vesicle found in the zoosporangia. The content of these vesicles undergoes dynamic changes during zoosporogenesis and during the late stages of sporogenesis the content becomes finely striated as is typical of these vesicles when observed in the zoospore. On the basis of the results presented here it is suggested that zoosporangium formation and zoosporogenesis in P. cubensis could serve as a model system for assays with obligate oomycetous plant pathogens, also in relation to fungicide mode of action studies.     

Sex differences in heritability of BMI: a comparative study of results from twin studies in eight countries.

Body mass index (BMI), a simple anthropometric measure, is the most frequently used measure of adiposity and has been instrumental in documenting the worldwide increase in the prevalence of obesity witnessed during the last decades. Although this increase in overweight and obesity is thought to be mainly due to environmental changes, i.e., sedentary lifestyles and high caloric diets, consistent evidence from twin studies demonstrates high heritability and the importance of genetic differences for normal variation in BMI. We analysed self-reported data on BMI from approximately 37,000 complete twin pairs (including opposite sex pairs) aged 20-29 and 30-39 from eight different twin registries participating in the GenomEUtwin project. Quantitative genetic analyses were conducted and sex differences were explored. Variation in BMI was greater for women than for men, and in both sexes was primarily explained by additive genetic variance in all countries. Sex differences in the variance components were consistently significant. Results from analyses of opposite sex pairs also showed evidence of sex-specific genetic effects suggesting there may be some differences between men and women in the genetic factors that influence variation in BMI. These results encourage the continued search for genes of importance to the body composition and the development of obesity. Furthermore, they suggest that strategies to identify predisposing genes may benefit from taking into account potential sex specific effects.